2X3T

Glutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crystal soaked with a synthetic glycopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.749 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Multivalent Binding to Wheat Germ Agglutinin.

Schwefel, D.Maierhofer, C.Beck, J.G.Seeberger, S.Diederichs, K.Moller, H.M.Welte, W.Wittmann, V.

(2010) J.Am.Chem.Soc. 132: 8704

  • DOI: 10.1021/ja101646k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The inhibition of carbohydrate-protein interactions by tailored multivalent ligands is a powerful strategy for the treatment of many human diseases. Crucial for the success of this approach is an understanding of the molecular mechanisms as to how a ...

    The inhibition of carbohydrate-protein interactions by tailored multivalent ligands is a powerful strategy for the treatment of many human diseases. Crucial for the success of this approach is an understanding of the molecular mechanisms as to how a binding enhancement of a multivalent ligand is achieved. We have synthesized a series of multivalent N-acetylglucosamine (GlcNAc) derivatives and studied their interaction with the plant lectin wheat germ agglutinin (WGA) by an enzyme-linked lectin assay (ELLA) and X-ray crystallography. The solution conformation of one ligand was determined by NMR spectroscopy. Employing a GlcNAc carbamate motif with alpha-configuration and by systematic variation of the spacer length, we were able to identify divalent ligands with unprecedented high WGA binding potency. The best divalent ligand has an IC(50) value of 9.8 microM (ELLA) corresponding to a relative potency of 2350 (1170 on a valency-corrected basis, i.e., per mol sugar contained) compared to free GlcNAc. X-ray crystallography of the complex of WGA and the second best, closely related divalent ligand explains this activity. Four divalent molecules simultaneously bind to WGA with each ligand bridging adjacent binding sites. This shows for the first time that all eight sugar binding sites of the WGA dimer are simultaneously functional. We also report a tetravalent neoglycopeptide with an IC(50) value of 0.9 microM being 25,500 times higher than that of GlcNAc (6400 times per contained sugar) and the X-ray structure analysis of its complex with glutaraldehyde-cross-linked WGA. Comparison of the crystal structure and the solution NMR structure of the neoglycopeptide as well as results from the ELLA suggest that the conformation of the glycopeptide in solution is already preorganized in a way supporting multivalent binding to the protein. Our findings show that bridging adjacent protein binding sites by multivalent ligands is a valid strategy to find high-affinity protein ligands and that even subtle changes of the linker structure can have a significant impact on the binding affinity.


    Organizational Affiliation

    Department of Biology, Universit├Ąt Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AGGLUTININ ISOLECTIN 1
A, B, C, D
171Triticum aestivumMutation(s): 0 
Find proteins for P10968 (Triticum aestivum)
Go to UniProtKB:  P10968
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLYCOPEPTIDE
E, M
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DBB
Query on DBB

Download SDF File 
Download CCD File 
A, B, C, D
D-ALPHA-AMINOBUTYRIC ACID
C4 H9 N O2
QWCKQJZIFLGMSD-GSVOUGTGSA-N
 Ligand Interaction
GYV
Query on GYV

Download SDF File 
Download CCD File 
A, B, C, D, E, M
2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DEOXY-ALPHA-D-GLUCOPYRANOSE
C9 H16 N2 O7
BMFDLZBABRHLIB-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
BAL
Query on BAL
E, M
peptide-likeC3 H7 N O2

--

DBB
Query on DBB
E, M
D-PEPTIDE LINKINGC4 H9 N O2

--

DVA
Query on DVA
E, M
D-PEPTIDE LINKINGC5 H11 N O2

--

PCA
Query on PCA
A, B, C, D
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.749 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.640α = 90.00
b = 93.210β = 98.32
c = 92.500γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Derived calculations, Non-polymer description, Refinement description, Version format compliance
  • Version 1.2: 2016-12-28
    Type: Source and taxonomy